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. 2017 Dec 1;16(12):4288-4298.
doi: 10.1021/acs.jproteome.7b00370. Epub 2017 Sep 15.

Proteomics Standards Initiative: Fifteen Years of Progress and Future Work

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Free PMC article

Proteomics Standards Initiative: Fifteen Years of Progress and Future Work

Eric W Deutsch et al. J Proteome Res. .
Free PMC article

Abstract

The Proteomics Standards Initiative (PSI) of the Human Proteome Organization (HUPO) has now been developing and promoting open community standards and software tools in the field of proteomics for 15 years. Under the guidance of the chair, cochairs, and other leadership positions, the PSI working groups are tasked with the development and maintenance of community standards via special workshops and ongoing work. Among the existing ratified standards, the PSI working groups continue to update PSI-MI XML, MITAB, mzML, mzIdentML, mzQuantML, mzTab, and the MIAPE (Minimum Information About a Proteomics Experiment) guidelines with the advance of new technologies and techniques. Furthermore, new standards are currently either in the final stages of completion (proBed and proBAM for proteogenomics results as well as PEFF) or in early stages of design (a spectral library standard format, a universal spectrum identifier, the qcML quality control format, and the Protein Expression Interface (PROXI) web services Application Programming Interface). In this work we review the current status of all of these aspects of the PSI, describe synergies with other efforts such as the ProteomeXchange Consortium, the Human Proteome Project, and the metabolomics community, and provide a look at future directions of the PSI.

Keywords: bioinformatics software; data standard; database; mass spectrometry; metabolomics; molecular interactions; protein identification; protein quantification; proteomics; quality control.

Conflict of interest statement

The authors declare no competing financial interest.

Figures

Figure 1
Figure 1
Overview of the relationship between PSI standard formats (blue rectangles), analysis steps (orange ovals), data repositories (purple cylinders), Application Programming Interfaces (green trapezoids), guidelines (white clipped rectangles), and other related resources described in this article. Resources with multiple prominent versions are decorated with those version numbers (gray for deprecated; blue for active; yellow for in development). Yellow elements are still early in the development process. Mass spectrometry formats are displayed relative to a typical MS workflow using standard formats.
Figure 2
Figure 2
Overview of the timeline of when PSI standards were published or released. Molecular interactions standards are depicted in the top half, while mass spectrometry standards are depicted in the bottom half. Shapes and colors are the same as described in the Figure 1 legend.

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